Seqmonk: Bedgraph as input ? (EPIC methylation array data)

Question

[Ankit]

Hi everyone,

Is it possible to give Bedgraph of methylation data as input to Seqmonk?

I do not have .cov or .bam. because the data is from EPIC methylation array. I only have Bedgraph.

I uploaded it as text file but it is not giving me strand separated view and rather like a line as in bed file. When I somehow quantitated no difference is observed in methylation pattern, which I clearly observed by UCSC view. I feel something is wrong in the way I am uploading.

I am also not sure how to design probe in seqmonk. I mean the window size, probe size ,step size for such kind of files.

If anyone have a suggestion or previous experience please help!

Thanks

[Ankit]

Any suggestions???? Thanks

[GenoMax]

Consider writing to SeqMonk team members directly.

Answer 1

[Charles Warden]

I'm not sure why you want to use Seqmonk for analysis of EPIC data.

However, these are some options that you have for EPIC data analysis:

GenomeStudio : pre-processing / beta calculation; some differential methylation

minfi : pre-processing / beta calculation; differential methylation, at either site or region level (with bumphunter)

COHCAP : primarily differential methylation (at site level, then region level)

RnBeads : QC plots; pre-processing and differential methylation